X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=402024b33ba32100b9f37854645aa5cfa13cce3c;hb=94175f47370a77a29184067438d77f11baae759e;hp=30e71b6f1df3f232353d1fb7bf8209d36f8224c6;hpb=f9f7150fdedd5899424b423ef564ca87ce28b96a;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 30e71b6..402024b 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -167,6 +167,7 @@ public class Commands
       for (ArgValue av : openAvList)
       {
         Arg a = av.getArg();
+        SubVals sv = av.getSubVals();
         String openFile = av.getValue();
         if (openFile == null)
           continue;
@@ -246,20 +247,24 @@ public class Commands
           af.setAnnotationsVisibility(showAnnotations, false, true);
 
           // wrap alignment?
-          if (avm.getBoolean(Arg.WRAP))
-          {
-            af.getCurrentView().setWrapAlignment(true);
-          }
+          boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
+                  null, "WRAP_ALIGNMENT", false);
+          af.getCurrentView().setWrapAlignment(wrap);
 
           // colour aligment?
-          if (avm.containsArg(Arg.COLOUR))
+          String colour = ArgParser.getFromSubValArgOrPref(avm, Arg.COLOUR,
+                  sv, null, "DEFAULT_COLOUR_PROT", "");
+
+          if ("" != colour)
           {
-            af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
+            af.changeColour_actionPerformed(colour);
           }
 
           // change alignment frame title
-          if (avm.containsArg(Arg.TITLE))
-            af.setTitle(avm.getValue(Arg.TITLE));
+          String title = ArgParser.getFromSubValArgOrPref(avm, Arg.TITLE,
+                  sv, null, null, null);
+          if (title != null)
+            af.setTitle(title);
 
           // show secondary structure annotations?
           boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,